National
Institute of Animal Health in Tsukuba, Japan has released a full set of
H5N8 sequences, A/chicken/Miyazaki/7/2014,
from a tracheal swab from a dead chicken in Miyazaki (collected
December 16). The sequences follow the recent release of another
full set of H5N8 sequences, A/crane/Kagoshima/KU1/2014,
from a tracheal swab of a sick white naped crane (collected November 23
by researchers at Kagoshima University). Both groups are
commended for the rapid release of these important sequences.Prior November H5N8 sequences
from healthy birds in Japan (A/duck/Chiba/26-372-48/2014
and A/duck/Chiba/26-372-61/2014) were Fujian clade 2.3.4.6, which had
evolved from the early 2014 outbreak in South Korea, and were very
closely related to November / December sequences from multiple
sites in multiple countries in Europe (Germany, Netherlands, England,
and Italy) including A/turkey/Germany-MV/R2472/2014,A/Ch/Netherlands/14015526, A/duck/England/36254/14, and A/turkey/Italy/14VIR7898-10/2014,
suggesting
migration from summer sites in Russia and/or Mongolia, which is supported
by a December
25 OIE report of the detection of H5N8 in a healthy Eurasian wigeon
shot in September in northeastern Russia (see map)
and tested in December. Sequences from that case have not been
released, but are similar to the cases in Europe and Japan.The two sets of recent
sequences from Japan are also Fujian clade 2.3.4.6, which evolved from
the sequences from South Korea, but are distinct from the earlier
sequences from Japan and Europe, as well as each other. All 8
gene segments fall into the same lineages as each of the above
sequences, but have independently evolved and represent unique
introductions leading to co-circulation of three distinct sub-clades in
Japan.The relationship of these
three subclades to the recently reported H5N2 and H5N8 outbreaks in Canada
and the United
States is unclear. The H5N8 reported from four dead
pet falcons in Lyndon, Washington, who had been fed a wigeon caught
near Wiser Lake, as well as the H5N8 at a small holding in Winston,
Oregon, were cited as having greater than 99% identity with the
South Korea sequences, for both H5 and N8 suggesting the sequences
matched the initial sequences from Japan and Europe. However, the
recent sequences leaves open the possibility that the US sequences
match the more recent distinct sub-clades represented by the sets
described above.This possibility is higher for
the H5N2 sequence from a northern pintail at Wiser Lake (see map),
which had an H5 that was only 98% identical to H5 from South
Korea. These US sequences were generated by the FDA, which
usually deposits sequences at Genbank, which doesn’t have the more
recent H5N8 sequences detailed above, which are at GISAID, so it is
unclear if the South Korean sequences are the closest match in the
public databases.Similarly, the CFIA in Canada
has noted that the H5N2 sequences in British Columbia have 5 H5N8 gene
segments, including Fujian H5, as well as 3 North American gene
segments, including N2, but the percent identity has not been cited and
the recent announcement on completion of sequences from multiple farms
did not cite the 5 to 3 ratio, leaving open the possibility of multiple
constellations associated with a Fujian H5 and a North American N2.The added complexity
introduced by the three distinct sub-clades in Japan, as well as the
announcement of H5N8 in northeast Russia in September, highlights the
need for the rapid release of sequences from Canada, United States, and
Russia.